Merge pull request #1719 from girder/closer-to-master

Merge master into the edit views ui branch
girder · Nov 7, 2024 · fbb2656 · fbb2656
2 parents 9ae784d + 1a7c504
commit fbb2656
Show file tree

Hide file tree

Showing 39 changed files with 901 additions and 208 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -5,7 +5,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
       - id: check-ast
@@ -58,21 +58,22 @@ repos:
     hooks:
       - id: circleci-config-validate
   - repo: https://github.com/ThisIsManta/stylus-supremacy
-    rev: v2.17.5
+    rev: v4.0.0
     hooks:
       - id: stylus-supremacy
+        language_version: "22.10.0"
         args:
           - '--options'
           - './girder/girder_large_image/web_client/package.json'
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.17.0
+    rev: v3.18.0
     hooks:
       - id: pyupgrade
         args:
           - --py38-plus
           - --keep-percent-format
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.1
+    rev: v0.7.0
     hooks:
       - id: ruff
         args:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,33 @@
 # Change Log
 
+## 1.30.3
+
+### Improvements
+
+- Format dates in item lists ([#1707](../../pull/1707))
+- Guard dtype types ([#1711](../../pull/1711), [#1714](../../pull/1714), [#1716](../../pull/1716))
+- Better handle IndicaLabs tiff files ([#1717](../../pull/1717))
+
+### Changes
+
+- Openslide now requires the binary wheel on appropriate platforms ([#1709](../../pull/1709), [#1710](../../pull/1710))
+
+## 1.30.2
+
+### Features
+
+- Support setting axis actual values in the zarr sink.  Display these in the frame selector ([#1625](../../pull/1625))
+
+### Improvements
+
+- Speed up recursive item lists ([#1694](../../pull/1694))
+- Better handle images with signed pixel data ([#1695](../../pull/1695))
+- Reduce loading geojs when switching views in Girder ([#1699](../../pull/1699))
+
+### Bug Fixes
+
+- Don't compute channel window in zarr sinks ([#1705](../../pull/1705))
+
 ## 1.30.1
 
 ### Improvements

diff --git a/docs/format_examples_datastore.py b/docs/format_examples_datastore.py
@@ -1,6 +1,7 @@
-import pooch
 from pathlib import Path
 
+import pooch
+
 EXAMPLES_FOLDER = Path('format_examples')
 
 format_examples = [

diff --git a/docs/generate_format_table.py b/docs/generate_format_table.py
@@ -1,7 +1,8 @@
-import large_image
 from pathlib import Path
-from format_examples_datastore import EXAMPLES_FOLDER, format_examples, fetch_all
 
+from format_examples_datastore import EXAMPLES_FOLDER, fetch_all, format_examples
+
+import large_image
 
 TABLE_FILE = Path('./format_table.rst')
 NO_MULTIFRAME_SOURCES = ['deepzoom', 'openjpeg', 'openslide']

diff --git a/docs/getting_started.rst b/docs/getting_started.rst
@@ -334,25 +334,60 @@ You can also composite a multi-frame image into a false-color output:
 Writing an Image
 ----------------
 
-If you wish to visualize numpy data, large_image can write a tiled tiff.  This requires a tile source that supports writing to be installed.  As of this writing, the ``large-image-source-zarr`` and ``large-image-source-vips`` sources supports this.  If both are installed, the ``large-image-source-zarr`` is the default.
+If you wish to visualize numpy data, ``large_image`` can write a tiled image.
+This requires a tile source that supports writing to be installed.
+As of this writing, the ``large-image-source-zarr`` and ``large-image-source-vips`` sources both support this.
+If both are installed, the ``large-image-source-zarr`` is the default.
+Some of the API options available for ``large-image-source-zarr`` are not available for ``large-image-source-vips``.
 
 .. code-block:: python
 
     import large_image
+
     source = large_image.new()
     for nparray, x, y in fancy_algorithm():
         # We could optionally add a mask to limit the output
         source.addTile(nparray, x, y)
     source.write('/tmp/sample.tiff', lossy=False)
 
-The ``large-image-source-zarr`` can be used to store multiple frame data with arbitrary axes.
+Multiple Frames
+~~~~~~~~~~~~~~~
+
+``large-image-source-zarr`` can be used to store multiframe data with arbitrary axes.
+The example below demonstrates the creation of an image with five axes: T, Z, Y, X, S.
 
 .. code-block:: python
 
     import large_image
+
+    time_values = [0.5, 1.5, 2.5, 3.5]
+    z_values = [3, 6, 9]
+    tile_pos_values = [0, 1024, 2048, 3072, 4096]
+
     source = large_image.new()
-    for nparray, x, y, time, param1 in fancy_algorithm():
-        source.addTile(nparray, x, y, time=time, p1=param1)
+    for t_index, t_value in enumerate(time_values):
+        for z_index, z_value in enumerate(z_values):
+            for y_value in tile_pos_values:
+                for x_value in tile_pos_values:
+
+                    # tile is a numpy array with shape (1024, 1024, 3)
+                    # this shape corresponds to the following axes, respectively: (Y, X, S)
+                    tile = get_my_data_tile(x_value, y_value, z_value, t_value)
+
+                    source.addTile(
+                        tile,
+                        x_value,
+                        y_value,
+                        z=z_index,
+                        time=t_index,
+
+                        # z_value and t_value are optional parameters to store the
+                        # true values at the provided z index and t index
+                        z_value=z_value,
+                        time_value=t_value,
+                    )
+    source.frameUnits = dict(t='ms', z='cm')
+
     # The writer supports a variety of formats
     source.write('/tmp/sample.zarr.zip', lossy=False)
 
@@ -361,31 +396,37 @@ You may also choose to read tiles from one source and write modified tiles to a
 .. code-block:: python
 
     import large_image
+
     original_source = large_image.open('path/to/original/image.tiff')
     new_source = large_image.new()
     for frame in original_source.getMetadata().get('frames', []):
         for tile in original_source.tileIterator(frame=frame['Frame'], format='numpy'):
-            t, x, y = tile['tile'], tile['x'], tile['y']
+            tile_data, x, y = tile['tile'], tile['x'], tile['y']
             kwargs = {
                 'z': frame['IndexZ'],
                 'c': frame['IndexC'],
             }
-            modified_tile = modify_tile(t)
+            modified_tile = modify_tile(tile_data)
             new_source.addTile(modified_tile, x=x, y=y, **kwargs)
     new_source.write('path/to/new/image.tiff', lossy=False)
 
+Multiple processes
+~~~~~~~~~~~~~~~~~~
+
 In some cases, it may be beneficial to write to a single image from multiple processes or threads:
 
 .. code-block:: python
 
     import large_image
     import multiprocessing
+
     # Important: Must be a pickleable function
     def add_tile_to_source(tilesource, nparray, position):
         tilesource.addTile(
             nparray,
             **position
         )
+
     source = large_image.new()
     # Important: Maximum size must be allocated before any multiprocess concurrency
     add_tile_to_source(source, np.zeros(1, 1, 3), dict(x=max_x, y=max_y, z=max_z))
@@ -397,4 +438,10 @@ In some cases, it may be beneficial to write to a single image from multiple pro
         )
     source.write('/tmp/sample.zarr.zip', lossy=False)
 
+
+More examples
+~~~~~~~~~~~~~
+
+To see more examples of using ``large-image-source-zarr`` to write images, see :doc:`notebooks` and the `Zarr Sink Tests <https://github.com/girder/large_image/blob/master/test/test_sink.py>`_.
+
 .. _Girder: https://girder.readthedocs.io/en/latest/
diff --git a/docs/girder_annotation_config_options.rst b/docs/girder_annotation_config_options.rst
@@ -32,7 +32,7 @@ This can be used to specify how annotations are listed on the item page.
       columns:
         -
           # The "record" type is from the default annotation record.  The value
-          # is one of "name", "creator", "created", "updatedId", "updated",
+          # is one of "name", "creator", "created", "updatedId", "updated".
           type: record
           value: name
         -
@@ -43,8 +43,9 @@ This can be used to specify how annotations are listed on the item page.
         -
           type: record
           value: created
-          # A format of date will use the browser's default date format
-          format: date
+          # A format of datetime, date, or time will use the browser's default
+          # date and/or time format
+          format: datetime
         -
           # The "metadata" type is taken from the annotations's
           # "annotation.attributes" contents.  It can be a nested key by using

diff --git a/docs/girder_config_options.rst b/docs/girder_config_options.rst
@@ -94,10 +94,14 @@ This is used to specify how items appear in item lists.  There are two settings,
       # clicking on an item from showing the item page to another action.
       navigate:
         # type can be "item": the default, open the item page, "itemList": go
-        # to the named item page
+        # to the named item page, or "open" to open an application
         type: itemList
         # if the type is "itemList", the name is the name of the itemList to
-        # display.
+        # display.  If the type is "open", the name is the name of the
+        # registered  application that should be opened by preference (e.g.,
+        # "histomicsui" or "volview").  If that application does not report it
+        # can open the item or no name is specified, the highest priority
+        # application that can open the item will be used.
         name: studyList
       # show these columns in order from left to right.  Each column has a
       # "type" and "value".  It optionally has a "title" used for the column
@@ -121,7 +125,8 @@ This is used to specify how items appear in item lists.  There are two settings,
           title: Slide Label
         -
           # The "record" type is from the default item record.  The value is
-          # one of "name", "size", or "controls".
+          # one of "name", "description", "created", "updated", "size", or
+          # "controls".
           type: record
           value: name
         -
@@ -135,8 +140,10 @@ This is used to specify how items appear in item lists.  There are two settings,
           # can be a nested key by using dots in its name.
           type: metadata
           value: Stain
-          # "format" can be "text", "number", "category".  Other values may be
-          # specified later.
+          # "format" can be "text", "number", "category", "datetime", "date",
+          # "time".  "datetime", "date", and "time" use the user's browser's
+          # locale to convert the date and/or time to their browser's preferred
+          # format.  Other values may be specified later.
           format: text
         -
           type: metadata